Flowering plants have evolved an enormous complexity and diversity in the developmental transition from vegetative to reproductive growth. Environmental and internal cues are integrated in a quantitative flowering response that varies between species and even between ecotypes (Anderson et al (2011) Trends Genet. 27: 258). Plants growing in temperate climates use photoperiod or day-length, in addition to vernalization or low temperatures to sense the passing of winter into optimal reproductive environmental conditions (Amasino et al (2010) Plant Physiol 154: 516). The elaboration of reproductive development in flowering plants is associated with the origin and diversification of developmental control genes, most prominently members of the MADS-box transcription factor family. The origin of several subfamilies of MADS-box genes with crucial roles in the floral transition remains shrouded in mystery, in that they appear to be present in just flowering plants or in specific lineages of flowering plants.
One lineage of MADS-box genes with a highly enigmatic origin is the clade of FLOWERING LOCUS C (FLC) genes. In the model plant Arabidopsis thaliana, FLC is a central repressor of the floral transition (Michaels & Amasino (1999) Plant Cell 11, 949), where it inhibits flowering by directly repressing the activity of central flowering promoters, namely SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1), FLOWERING LOCUS D (FD) and FLOWERING LOCUS T (FT) (Anderson et al (2011) (supra); Amasino et al (2010) (supra); Michaels & Amasino (1999) (supra); Adrian et al (2009) Mol. Plant. 2, 628; Searle et al (2006) Genes. Dev. 20, 898). Vernalization alleviates this repression by negatively regulating FLC expression through epigenetic modifications of the chromatin structure at the FLC locus (Amasino et al (2010) (supra); Adrian et al (2009) (supra). FLC also transduces temperature signals during seed germination Chiang et al (2009) Proc Natl Acad Sci USA 106:11661). FLC has five closely related paralogs in the Arabidopsis thaliana genome, some of which also act as floral repressors (Ratcliffe et al (2001) Plant Physiol. 126, 122; Ratcliffe et al (2003) Plant Cell 15, 1159; Kim & Sung (2010) Proc. Natl. Acad. Sci. USA. 107, 17029). These paralogs arose in evolution through sequential tandem and genome duplications within the order Brassicales (Schranz et al (2002) Genetics, 162, 1457; Nah & Chen (2010) New Phytol. 186, 228). Tandem duplications of FLC-like genes appear not uncommon, as they have also been reported in other Arabidopsis species (Nah & Chen (2010) (supra). Outside of Brassicales FLC-like genes have been identified in more distantly related core eudicot species. For instance in sugar beet (Beta vulgaris), a crop with a strong vernalization requirement, FLC expression also responds to vernalization. This suggests that FLC's role in cold-induced flowering is conserved in core eudicots (Reeves et al (2007) Genetics 176, 295). FLC homologs, however, have not been identified outside the core eudicots and the phylogenetic position of this subfamily in the larger MADS-box gene phylogeny, and therefore its evolutionary origin, is uncertain. It has therefore been postulated that FLC genes do not exist in monocots and current models for the regulation of flowering time in cereals do not include FLC (Alexandre & Hennig (2008) J. Exp. Bot. 59, 1127; Colasanti & Coneva (2009) Plant Physiol. 149: 56-62, Jarillo & Pineiro (2011) Plant Sci. 181: 364-378; Yan et al (2003) PNAS 100:6263-6268; Yan et al (2004) Science 303:1640-1644; Yan et al (2006) PNAS 103:19581-19586; Cockram et al (2007) J Exp Bot 58:1231-1244). Historically, vernalization has been first described and extensively studied in temperate monocot crops, like winter varieties of wheat and barley (Chouard (1960) Annu. Rev. Plant Physiol. 11, 191). This illustrates the agronomic importance of this trait. To significantly accelerate flowering and subsequent seed set, winter cereals require a sufficiently long period of cold. In contrast to Arabidopsis, however, the currently known elements of their vernalization response only involve other members of the MADS-box gene family as well as other genes (Chouard (1960) (supra); Alexandre & Hennig (2008), supra; Kim et al (2009) Annu. Rev. Cell Dev. Biol. 25, 277). Therefore, it has previously been suggested that the vernalization response in temperate cereals and eudicots has evolved independently (Alexandre & Hennig (2008) (supra); Kim et al (2009) (supra); Hemming & Trevaskis (2011) Plant Sci. 180, 447; Ream et al. (2013) Cold Spring Harb. Symp. Quant. Biol. doi:10.1101/sqb.2013.77.014449) and, hence, do not commonly involve FLC.
FLC-like genes are not the only subfamily of MADS-box genes with an enigmatic origin. While members of the SQUAMOSA (SQUA) and SEPALLATA (SEP) subfamilies have been identified in all major flowering plant lineages, no gymnosperm representatives have so far been found despite the availability of extensive transcriptome data and targeted cloning efforts Rigault et al. (2011) Plant Physiol. 157:14-28; Melzer et al (2010) Semin. Cell Dev Biol. 21:118-128. In angiosperms, rounds of polyploidization (whole-genome duplications) probably generated many of the observed gene duplications in the SQUA and SEP subfamilies (Veron et al. (2007), Mol. Biol. Evol. 24:670-678; Shan et al (2009) Mol. Biol. Evol. 26:2229-2244; Jiao et al (2012) Genome Biol. 13:R3; Vekemans et al. (2012) Mol. Biol. Evol. doi: 10.1093/molbev/mss183). Members of the SQUA subfamily are generally positive regulators of the floral transition since they control the formation of inflorescence and floral meristems (Bowman et al (1993) Development, 119(3):721-743). SEP genes act as key regulators of floral organ specification, and in a partially redundant manner with SQUA-like genes in floral meristem specification (Pelaz et al (2000) Nature 405:200-203; Kaufmann et al. (2009) PLoS Biol. 7, e1000090).
Greenup e al. ((2010) Plant Physiol. 153, 1062) describes the identification of a vernalization responsive barley MADS box floral repressor protein.
Winfield et al ((2009) BMC Plant Biol. 9, 55) describes cold- and light-induced changes in the transcriptome of wheat leading to phase transition from vegetative to reproductive growth.
WO2006/068432 discloses to flowering-time and/or stem elongation regulator isolated from rice, a DNA construct containing the regulator, a transgenic plant, a part thereof, and plant cell transformed with the DNA construct, and methods to control flowering-time and/or stem elongation using the regulator.
Clarifying the origin of the enigmatic FLC subfamily, but also that of SEP and SQUA can greatly contribute to our understanding of the evolution of flowering plants. Here, we combined genomic synteny-based approaches and phylogeny reconstruction to understand the evolutionary history of these MADS-box gene subfamilies. This allowed us to identify FLC orthologs in monocots. Similar to Arabidopsis FLC, the expression of these FLC-like genes is responsive to a prolonged cold period. The identified tandem arrangement of the FLC, SEP and SQUA subfamilies suggests an origin of these subfamilies by an ancient tandem duplication prior to the origin of extant flowering plants, followed by segmental duplications linked to rounds of polyploidization. Our results close an important gap in our understanding on the origin of developmental key regulatory genes in flowering plants.